Contacts of the helix formed by residues 536 - 544 (chain S) in PDB entry 1I84
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 536 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526S GLU 3.5 9.9 - - - -
527S LEU 3.5 9.6 - - - -
528S ILE* 3.9 4.5 - - - -
530S ARG 2.8 21.5 + - - -
535S PRO* 1.3 74.7 - - - +
537S VAL* 1.3 69.3 + - - +
538S LEU 3.0 3.1 - - - -
539S ALA* 2.8 18.4 + - - +
540S LEU* 3.3 8.9 + - - +
563S GLN* 4.6 1.3 - - - -
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Residues in contact with VAL 537 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480S LEU* 4.2 9.0 - - + -
527S LEU* 2.8 43.8 + - + +
528S ILE* 3.5 13.5 - - + +
536S GLY* 1.3 71.3 - - - +
538S LEU* 1.3 63.4 + - - +
540S LEU* 3.8 0.7 + - - +
541S LEU* 3.4 20.8 + - - +
555S PHE* 3.8 4.0 - - + -
559S LEU* 3.9 23.3 - - + -
563S GLN* 4.8 3.3 - - + +
581S PHE* 3.7 38.4 - - + -
583S ILE* 4.9 4.3 - - + -
597S TRP* 4.0 13.2 - - + -
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Residues in contact with LEU 538 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477S PHE* 3.4 37.9 - - + -
480S LEU* 5.1 1.1 - - + -
481S CYS* 5.3 5.8 - - + -
484S TYR* 4.7 14.6 - - + -
528S ILE* 3.4 34.7 + - + +
529S GLU 5.4 0.4 - - - +
536S GLY 3.0 0.6 - - - -
537S VAL* 1.3 76.6 - - - +
539S ALA* 1.3 61.9 + - - +
541S LEU* 3.6 4.4 + - - +
542S ASP* 2.7 39.4 + - - +
601S ASN* 4.7 2.7 - - - +
660S GLY* 3.7 31.6 - - - +
663S TYR* 5.8 2.9 - - + -
664S LYS* 4.6 23.1 - - + +
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Residues in contact with ALA 539 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529S GLU 5.5 1.0 + - - +
530S ARG 4.0 8.0 + - - +
531S PRO* 4.3 13.0 - - + +
535S PRO* 3.9 11.2 - - + -
536S GLY 2.8 31.8 + - - +
538S LEU* 1.3 72.1 - - - +
540S LEU* 1.3 65.4 + - + +
542S ASP* 2.7 27.5 + - - +
543S GLU* 3.3 6.4 + - - +
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Residues in contact with LEU 540 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535S PRO* 3.3 30.1 - - + -
536S GLY 3.3 12.1 + - - +
537S VAL 4.1 0.7 - - - +
539S ALA* 1.3 73.2 - - - +
541S LEU* 1.3 55.3 + - - +
542S ASP 2.4 14.9 + - - -
543S GLU* 2.9 29.6 + - - +
544S GLU* 3.0 15.9 + - - -
555S PHE* 3.7 12.1 - - + -
558S LYS* 4.9 11.4 - - + -
559S LEU* 3.4 41.7 - - + +
561S GLN* 4.7 3.6 - - - +
562S GLU* 4.0 22.0 - - + -
563S GLN* 4.3 7.4 - - - +
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Residues in contact with LEU 541 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477S PHE* 4.1 11.2 - - + -
537S VAL 3.4 9.2 + - - +
538S LEU* 3.8 3.4 - - + +
539S ALA 3.4 0.6 - - - -
540S LEU* 1.3 75.3 - - - +
542S ASP* 1.3 56.5 + - - +
544S GLU* 4.6 0.2 - - - -
545S CYS* 2.9 23.1 - - - +
552S ASP* 5.2 0.4 - - - +
555S PHE* 3.2 49.9 - - + -
597S TRP* 3.4 51.4 - - + +
598S LEU* 3.4 18.7 - - + +
601S ASN* 3.0 31.0 + - + +
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Residues in contact with ASP 542 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538S LEU* 2.7 31.3 - - - +
539S ALA* 2.7 18.2 + - - +
540S LEU 2.4 12.9 + - - -
541S LEU* 1.3 67.2 - - - +
543S GLU* 1.3 59.0 + - - +
545S CYS* 3.0 23.0 - - - +
546S TRP* 3.8 13.2 + - + -
601S ASN* 3.2 14.3 + - - +
658S THR* 2.9 36.2 + - + +
660S GLY* 4.5 5.8 - - - -
661S GLN* 4.3 18.2 + - - -
664S LYS* 6.0 0.3 - - - -
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Residues in contact with GLU 543 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539S ALA 3.3 4.0 + - - +
540S LEU* 2.9 25.2 + - - +
542S ASP* 1.3 73.6 - - - +
544S GLU* 1.3 84.4 + - - +
545S CYS 2.7 5.5 + - - -
546S TRP* 2.4 45.0 + - - +
547S PHE* 4.6 1.4 - - + +
558S LYS* 4.0 14.3 - - - -
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Residues in contact with GLU 544 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540S LEU 3.0 14.7 + - - +
541S LEU* 4.6 4.0 - - - -
543S GLU* 1.3 95.7 + - - +
545S CYS* 1.3 57.2 + - - +
546S TRP 3.2 0.4 - - - -
547S PHE* 4.3 16.7 - - + +
550S ALA* 3.0 34.7 - - - +
554S SER* 3.1 24.8 + - - +
555S PHE* 3.9 19.9 + - + +
558S LYS* 3.5 32.7 + - + +
598S LEU* 3.6 9.7 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il